Milk and dairy products are important sources of nutrients in the human diet because they contain a number of essential substances and other biologically active components. Many of these substances can be modified, and thus offer opportunities to use milk and dairy products as functional food. Isoflavones are particularly important in human nutrition due to their diverse pharmacological and antioxidant properties. The clinical effectiveness of isoflavone-rich products is believed to be dependent on their ability to metabolize daidzein to equol, which may directly exert cancer preventive effects. However, only approximately 30–40% of humans are able to produce equol, while animals, in general, produce equol. Equol is the predominant product of bacterial metabolism of isoflavones and can be found in various amounts in some food of animal origin, especially in milk. Therefore, milk and dairy products can be considered to be sources of equol for humans who are not able to produce this metabolite. When the content of isoflavones in milk is to be modified, two groups of factors should be considered, i.e., dietary factors that include the source of isoflavones and the processing effects on feedstuffs and animal factors that include the intake of isoflavones, ruminal and postruminal changes, and the health and physiological status of animals. The approximate content of isoflavones in milk can be predicted using carry-over rates for different dietary sources or using a formula that describes the relationship between equol concentration in milk and formononetin intake. Processing and storage can affect the content and profile of isoflavones in milk and dairy products.